Parametric design for pen adapter for 3D printing
I understand your problem to be:
"How do I make this model parametric, so people don't need to change vertices in order to adapt it to their physiology"

Here I have a few pointers:


The question of the pen is probably the easiest solution: Create a mesh for a pen and use a boolien modifier to create the hole. Each grip can be scaled but the hole for the pencil will remain the same size.
Unless blender implements an node based modelling toolkit in the near future, your toolkit in order of ease to use consists of:


shape-keys Morph targets: A sphere shape turning into a cylindrical unwrapped sphere shape
boolean modifiers
scripts